rstudio: clean up and refactor (#357034)

diff --git a/src/cpp/core/libclang/LibClang.cpp b/src/cpp/core/libclang/LibClang.cpp

index f166a43b37..d8024b2ce7 100644

--- a/src/cpp/core/libclang/LibClang.cpp

+++ b/src/cpp/core/libclang/LibClang.cpp

@@ -62,7 +62,7 @@

    // we need to add in the associated libclang headers as

    // they are not discovered / used by default during compilation

-   FilePath llvmPath = s_libraryPath.getParent().getParent();

+   FilePath llvmPath("@libclang@");

    boost::format fmt("%1%/lib/clang/%2%/include");

    fmt % llvmPath.getAbsolutePath() % version.asString();

    std::string includePath = fmt.str();

@@ -74,47 +74,7 @@

 std::vector<std::string> systemClangVersions()

 {

-   std::vector<std::string> clangVersions;

-   

-#if defined(__APPLE__)

-   // NOTE: the version of libclang.dylib bundled with Xcode

-   // doesn't seem to work well when loaded as a library

-   // (there seems to be extra orchestration required to get

-   // include paths set up; easier to just depend on command

-   // line tools since we request their installation in other

-   // contexts as well)

-   clangVersions = {

@@ -84,34 +84,13 @@ std::vector<std::string> systemClangVersions()

    // line tools since we request their installation in other

    // contexts as well)

    clangVersions = {

-      "/Library/Developer/CommandLineTools/usr/lib/libclang.dylib"

-   };

-#elif defined(__unix__)

-   // default set of versions

-   clangVersions = {

+      "@libclang@/lib/libclang.dylib"

    };

 #elif defined(__unix__)

    // default set of versions

    clangVersions = {

-      "/usr/lib/libclang.so",

-      "/usr/lib/llvm/libclang.so",

-      "/usr/lib64/libclang.so",

-      "/usr/lib64/llvm/libclang.so",

-   };

+      "@libclang@/lib/libclang.so",

    };

-   

-   // iterate through the set of available 'llvm' directories

-   for (const char* prefix : {"/usr/lib", "/usr/lib64"})

-         if (path.getFilename().find("llvm") == 0)

-            clangVersions.push_back(path.completePath("lib/libclang.so.1").getAbsolutePath());

-   }

-#endif

-   

-   return clangVersions;

+    return std::vector<std::string> { "@libclang.so@" };

 }

 #endif

    return clangVersions;

{ lib

, stdenv

, mkDerivation

, fetchurl

, fetchFromGitHub

, makeDesktopItem

, copyDesktopItems

, cmake

, boost183

, zlib

, openssl

, R

, qtbase

, qtxmlpatterns

, qtsensors

, qtwebengine

, qtwebchannel

, quarto

, libuuid

, hunspellDicts

, unzip

, ant

, jdk

, gnumake

, pandoc

, llvmPackages

, yaml-cpp

, soci

, postgresql

, nodejs

, qmake

, server ? false # build server version

, sqlite

, pam

, nixosTests

{

  lib,

  stdenv,

  fetchzip,

  fetchFromGitHub,

  replaceVars,

  cmake,

  boost183,

  zlib,

  openssl,

  R,

  libsForQt5,

  quarto,

  libuuid,

  hunspellDicts,

  ant,

  jdk,

  gnumake,

  pandoc,

  llvmPackages,

  yaml-cpp,

  soci,

  sqlite,

  nodejs,

  yarn,

  yarnConfigHook,

  fetchYarnDeps,

  server ? false, # build server version

  pam,

  nixosTests,

}:

let

  pname = "RStudio";

  version = "2024.04.2+764";

  RSTUDIO_VERSION_MAJOR = lib.versions.major version;

  RSTUDIO_VERSION_MINOR = lib.versions.minor version;

  RSTUDIO_VERSION_PATCH = lib.versions.patch version;

  RSTUDIO_VERSION_SUFFIX = "+" + toString (

    lib.tail (lib.splitString "+" version)

  );

  src = fetchFromGitHub {

    owner = "rstudio";

    repo = "rstudio";

    rev = "v" + version;

    hash = "sha256-j258eW1MYQrB6kkpjyolXdNuwQ3zSWv9so4q0QLsZuw=";

  };

  mathJaxSrc = fetchurl {

  mathJaxSrc = fetchzip {

    url = "https://s3.amazonaws.com/rstudio-buildtools/mathjax-27.zip";

    hash = "sha256-xWy6psTOA8H8uusrXqPDEtL7diajYCVHcMvLiPsgQXY=";

  };

  rsconnectSrc = fetchFromGitHub {

    owner = "rstudio";

    repo = "rsconnect";

    rev = "v1.2.2";

    hash = "sha256-wvM9Bm7Nb6yU9z0o+uF5lB2kdgjOW5wZSk6y48NPF2U=";

    hash = "sha256-J7SZK/9q3HcXTD7WFHxvh++ttuCd89Vc4SEBrUEU0AI=";

  };

  # Ideally, rev should match the rstudio release name.

    hash = "sha256-lZnZvioztbBWWa6H177X6rRrrgACx2gMjVFDgNup93g=";

  };

  description = "Set of integrated tools for the R language";

  hunspellDictionaries = lib.filter lib.isDerivation (lib.unique (lib.attrValues hunspellDicts));

  # These dicts contain identically-named dict files, so we only keep the

  # -large versions in case of clashes

  largeDicts = lib.filter (d: lib.hasInfix "-large-wordlist" d.name) hunspellDictionaries;

  otherDicts = lib.filter (

    d: !(lib.hasAttr "dictFileName" d && lib.elem d.dictFileName (map (d: d.dictFileName) largeDicts))

  ) hunspellDictionaries;

  dictionaries = largeDicts ++ otherDicts;

in

(if server then stdenv.mkDerivation else mkDerivation)

  (rec {

    inherit pname version src RSTUDIO_VERSION_MAJOR RSTUDIO_VERSION_MINOR RSTUDIO_VERSION_PATCH RSTUDIO_VERSION_SUFFIX;

stdenv.mkDerivation rec {

  pname = "RStudio";

  version = "2024.04.2+764";

  RSTUDIO_VERSION_MAJOR = lib.versions.major version;

  RSTUDIO_VERSION_MINOR = lib.versions.minor version;

  RSTUDIO_VERSION_PATCH = lib.versions.patch version;

  RSTUDIO_VERSION_SUFFIX = "+" + toString (lib.tail (lib.splitString "+" version));

    nativeBuildInputs = [

  src = fetchFromGitHub {

    owner = "rstudio";

    repo = "rstudio";

    rev = "refs/tags/v${version}";

    hash = "sha256-j258eW1MYQrB6kkpjyolXdNuwQ3zSWv9so4q0QLsZuw=";

  };

  nativeBuildInputs =

    [

      cmake

      unzip

      ant

      jdk

      pandoc

      nodejs

    ] ++ lib.optionals (!server) [

      copyDesktopItems

      yarn

      yarnConfigHook

    ]

    ++ lib.optionals (!server) [

      libsForQt5.wrapQtAppsHook

    ];

    buildInputs = [

  buildInputs =

    [

      boost183

      zlib

      openssl

      libuuid

      yaml-cpp

      soci

      postgresql

      quarto

    ] ++ (if server then [

      sqlite.dev

      pam

    ] else [

      qtbase

      qtxmlpatterns

      qtsensors

      qtwebengine

      qtwebchannel

    ]);

    cmakeFlags = [

      "-DRSTUDIO_TARGET=${if server then "Server" else "Desktop"}"

      "-DRSTUDIO_USE_SYSTEM_SOCI=ON"

      "-DRSTUDIO_USE_SYSTEM_BOOST=ON"

      "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON"

      "-DRSTUDIO_DISABLE_CHECK_FOR_UPDATES=ON"

      "-DQUARTO_ENABLED=TRUE"

      "-DPANDOC_VERSION=${pandoc.version}"

      "-DCMAKE_INSTALL_PREFIX=${placeholder "out"}/lib/rstudio"

    ] ++ lib.optionals (!server) [

      "-DQT_QMAKE_EXECUTABLE=${qmake}/bin/qmake"

    ]

    ++ lib.optionals server [ pam ]

    ++ lib.optionals (!server) [

      libsForQt5.qtbase

      libsForQt5.qtxmlpatterns

      libsForQt5.qtsensors

      libsForQt5.qtwebengine

      libsForQt5.qtwebchannel

    ];

  cmakeFlags =

    [

      (lib.cmakeFeature "RSTUDIO_TARGET" (if server then "Server" else "Desktop"))

      (lib.cmakeBool "RSTUDIO_USE_SYSTEM_SOCI" true)

      (lib.cmakeBool "RSTUDIO_USE_SYSTEM_BOOST" true)

      (lib.cmakeBool "RSTUDIO_USE_SYSTEM_YAML_CPP" true)

      (lib.cmakeBool "RSTUDIO_DISABLE_CHECK_FOR_UPDATES" true)

      (lib.cmakeBool "QUARTO_ENABLED" true)

      (lib.cmakeFeature "CMAKE_INSTALL_PREFIX" "${placeholder "out"}/lib/rstudio")

    ]

    ++ lib.optionals (!server) [

      (lib.cmakeFeature "QT_QMAKE_EXECUTABLE" "${libsForQt5.qmake}/bin/qmake")

      (lib.cmakeBool "RSTUDIO_INSTALL_FREEDESKTOP" true)

    ];

    # Hack RStudio to only use the input R and provided libclang.

  patches = [

      ./r-location.patch

      ./clang-location.patch

      ./use-system-node.patch

    # Hack RStudio to only use the input R and provided libclang.

    (replaceVars ./r-location.patch {

      R = lib.getBin R;

    })

    (replaceVars ./clang-location.patch {

      libclang = lib.getLib llvmPackages.libclang;

    })

    ./fix-resources-path.patch

      ./pandoc-nix-path.patch

      ./use-system-quarto.patch

    ./ignore-etc-os-release.patch

    ./dont-yarn-install.patch

    ./dont-assume-pandoc-in-quarto.patch

  ];

  postPatch = ''

      substituteInPlace src/cpp/core/r_util/REnvironmentPosix.cpp --replace-fail '@R@' ${R}

    # fix .desktop Exec field

    substituteInPlace src/node/desktop/resources/freedesktop/rstudio.desktop.in \

      --replace-fail "''${CMAKE_INSTALL_PREFIX}/rstudio" "rstudio"

      substituteInPlace src/gwt/build.xml \

        --replace-fail '@node@' ${nodejs} \

        --replace-fail './lib/quarto' ${quartoSrc}

    # set install path of freedesktop files

    substituteInPlace src/{cpp,node}/desktop/CMakeLists.txt \

      --replace-fail "/usr/share" "$out/share"

  '';

      substituteInPlace src/cpp/conf/rsession-dev.conf \

        --replace-fail '@node@' ${nodejs}

  yarnOfflineCache = fetchYarnDeps {

    yarnLock = quartoSrc + "/yarn.lock";

    hash = "sha256-Qw8O1Jzl2EO0DEF3Jrw/cIT9t22zs3jyKgDA5XZbuGA=";

  };

      substituteInPlace src/cpp/core/libclang/LibClang.cpp \

        --replace-fail '@libclang@' ${lib.getLib llvmPackages.libclang} \

        --replace-fail '@libclang.so@' ${lib.getLib llvmPackages.libclang}/lib/libclang.so

  dontYarnInstallDeps = true; # will call manually in preConfigure

      substituteInPlace src/cpp/session/CMakeLists.txt \

        --replace-fail '@pandoc@' ${pandoc} \

        --replace-fail '@quarto@' ${quarto}

  preConfigure = ''

    # set up node_modules directory inside quarto so that panmirror can be built

    mkdir src/gwt/lib/quarto

    cp -r --no-preserve=all ${quartoSrc}/* src/gwt/lib/quarto

    pushd src/gwt/lib/quarto

    yarnConfigHook

    popd

      substituteInPlace src/cpp/session/include/session/SessionConstants.hpp \

        --replace-fail '@pandoc@' ${pandoc}/bin \

        --replace-fail '@quarto@' ${quarto}

    '';

    ### set up dependencies that will be copied into the result

    # note: only the directory names have to match upstream, the actual versions don't

    # note: symlinks are preserved

    hunspellDictionaries = lib.filter lib.isDerivation (lib.unique (lib.attrValues hunspellDicts));

    # These dicts contain identically-named dict files, so we only keep the

    # -large versions in case of clashes

    largeDicts = lib.filter (d: lib.hasInfix "-large-wordlist" d.name) hunspellDictionaries;

    otherDicts = lib.filter

      (d: !(lib.hasAttr "dictFileName" d &&

        lib.elem d.dictFileName (map (d: d.dictFileName) largeDicts)))

      hunspellDictionaries;

    dictionaries = largeDicts ++ otherDicts;

    preConfigure = ''

    mkdir dependencies/dictionaries

    for dict in ${builtins.concatStringsSep " " dictionaries}; do

      for i in "$dict/share/hunspell/"*; do

      done

    done

      unzip -q ${mathJaxSrc} -d dependencies/mathjax-27

    ln -s ${quarto} dependencies/quarto

     # As of Chocolate Cosmos, node 18.20.3 is used for runtime

     # 18.18.2 is still used for build

     # see https://github.com/rstudio/rstudio/commit/facb5cf1ab38fe77813aaf36590804e4f865d780

     mkdir -p dependencies/common/node/18.20.3

    # version in dependencies/common/install-mathjax

    ln -s ${mathJaxSrc} dependencies/mathjax-27

      mkdir -p dependencies/pandoc/${pandoc.version}

      cp ${pandoc}/bin/pandoc dependencies/pandoc/${pandoc.version}/pandoc

    # version in CMakeGlobals.txt (PANDOC_VERSION)

    mkdir -p dependencies/pandoc/2.18

    ln -s ${lib.getBin pandoc}/bin/* dependencies/pandoc/2.18

      cp -r ${rsconnectSrc} dependencies/rsconnect

      ( cd dependencies && ${R}/bin/R CMD build -d --no-build-vignettes rsconnect )

    # version in CMakeGlobals.txt (RSTUDIO_INSTALLED_NODE_VERSION)

    mkdir -p dependencies/common/node

    ln -s ${nodejs} dependencies/common/node/18.20.3

  '';

  postInstall = ''

      mkdir -p $out/bin $out/share

    mkdir -p $out/bin

      ${lib.optionalString (!server) ''

        mkdir -p $out/share/icons/hicolor/48x48/apps

        ln $out/lib/rstudio/rstudio.png $out/share/icons/hicolor/48x48/apps

    ${lib.optionalString server ''

      ln -s $out/lib/rstudio/bin/{crash-handler-proxy,postback,r-ldpath,rpostback,rserver,rserver-pam,rsession,rstudio-server} $out/bin

    ''}

      for f in {${if server

        then "crash-handler-proxy,postback,r-ldpath,rpostback,rserver,rserver-pam,rsession,rstudio-server"

        else "diagnostics,rpostback,rstudio"}}; do

        ln -s $out/lib/rstudio/bin/$f $out/bin

      done

    ${lib.optionalString (!server) ''

      ln -s $out/lib/rstudio/bin/{diagnostics,rpostback,rstudio} $out/bin

    ''}

  '';

      for f in .gitignore .Rbuildignore LICENSE README; do

        find . -name $f -delete

      done

  qtWrapperArgs = lib.optionals (!server) [

    "--suffix PATH : ${lib.makeBinPath [ gnumake ]}"

  ];

      rm -r $out/lib/rstudio/{INSTALL,COPYING,NOTICE,README.md,SOURCE,VERSION}

    '';

  passthru = {

    inherit server;

    tests = {

      inherit (nixosTests) rstudio-server;

    };

  };

  meta = {

    broken = (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64);

      inherit description;

    description = "Set of integrated tools for the R language";

    homepage = "https://www.rstudio.com/";

    license = lib.licenses.agpl3Only;

      maintainers = with lib.maintainers; [ ciil cfhammill ];

    maintainers = with lib.maintainers; [

      ciil

      cfhammill

    ];

    mainProgram = "rstudio" + lib.optionalString server "-server";

    platforms = lib.platforms.linux;

  };

    passthru = {

      inherit server;

      tests = { inherit (nixosTests) rstudio-server; };

    };

  } // lib.optionalAttrs (!server) {

    qtWrapperArgs = [

      "--suffix PATH : ${lib.makeBinPath [ gnumake ]}"

    ];

    desktopItems = [

      (makeDesktopItem {

        name = pname;

        exec = "rstudio %F";

        icon = "rstudio";

        desktopName = "RStudio";

        genericName = "IDE";

        comment = description;

        categories = [ "Development" ];

        mimeTypes = [

          "text/x-r-source" "text/x-r" "text/x-R" "text/x-r-doc" "text/x-r-sweave" "text/x-r-markdown"

          "text/x-r-html" "text/x-r-presentation" "application/x-r-data" "application/x-r-project"

          "text/x-r-history" "text/x-r-profile" "text/x-tex" "text/x-markdown" "text/html"

          "text/css" "text/javascript" "text/x-chdr" "text/x-csrc" "text/x-c++hdr" "text/x-c++src"

        ];

      })

    ];

  })

}

diff --git a/src/cpp/session/CMakeLists.txt b/src/cpp/session/CMakeLists.txt

index 0202e84..596b9f8 100644

--- a/src/cpp/session/CMakeLists.txt

+++ b/src/cpp/session/CMakeLists.txt

@@ -59,11 +59,7 @@ endif()

 # install pandoc

-# - by default, we use quarto + quarto's bundled pandoc

-# - if quarto is not enabled, use pandoc fallback

-if(QUARTO_ENABLED)

-   set(RSTUDIO_DEPENDENCIES_PANDOC_DIR "${RSTUDIO_DEPENDENCIES_QUARTO_DIR}/bin/tools")

-elseif(EXISTS "${RSTUDIO_TOOLS_ROOT}/pandoc/${PANDOC_VERSION}")

+if(EXISTS "${RSTUDIO_TOOLS_ROOT}/pandoc/${PANDOC_VERSION}")

    set(RSTUDIO_DEPENDENCIES_PANDOC_DIR "${RSTUDIO_TOOLS_ROOT}/pandoc/${PANDOC_VERSION}")

 else()

    set(RSTUDIO_DEPENDENCIES_PANDOC_DIR "${RSTUDIO_DEPENDENCIES_DIR}/pandoc/${PANDOC_VERSION}")

@@ -733,11 +729,10 @@ if(NOT RSTUDIO_SESSION_WIN32 AND NOT RSESSION_ALTERNATE_BUILD)

                PATTERN ".gitignore"

                EXCLUDE)

       endif()

-   else()

-      install(DIRECTORY "${RSTUDIO_DEPENDENCIES_PANDOC_DIR}/"

-              DESTINATION "${RSTUDIO_INSTALL_BIN}/pandoc"

-              USE_SOURCE_PERMISSIONS)

    endif()

+   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_PANDOC_DIR}/"

+           DESTINATION "${RSTUDIO_INSTALL_BIN}/pandoc"

+           USE_SOURCE_PERMISSIONS)

    # install embedded packages

    foreach(PKG ${RSTUDIO_EMBEDDED_PACKAGES})

diff --git a/src/cpp/session/include/session/SessionConstants.hpp b/src/cpp/session/include/session/SessionConstants.hpp

index e6aef22..57491ec 100644

--- a/src/cpp/session/include/session/SessionConstants.hpp

+++ b/src/cpp/session/include/session/SessionConstants.hpp

@@ -147,11 +147,7 @@

 #define kSessionTmpDirEnvVar       "RS_SESSION_TMP_DIR"

 #define kSessionTmpDir             "rstudio-rsession"

-#ifdef QUARTO_ENABLED

-# define kDefaultPandocPath        "bin/quarto/bin/tools"

-#else

 # define kDefaultPandocPath        "bin/pandoc"

-#endif

 #define kDefaultNodePath           "bin/node"

 #define kDefaultQuartoPath         "bin/quarto"

diff --git a/src/gwt/build.xml b/src/gwt/build.xml

index 27ffe33..4218678 100644

--- a/src/gwt/build.xml

+++ b/src/gwt/build.xml

@@ -139,11 +139,6 @@

       <echo message="panmirror minify: ${panmirror.minify}"/>

       <mkdir dir="${panmirror.build.dir}"/>

-      <exec executable="${yarn.bin}" dir="${panmirror.dir}" resolveexecutable="true" failonerror="true">

-         <arg value="install"/>

-         <arg value="--network-timeout"/>

-         <arg value="240000"/>

-      </exec>

       <exec executable="${yarn.bin}" dir="${panmirror.dir}" resolveexecutable="true" failonerror="true">

          <arg value="build"/>

          <arg value="--minify"/>

--- a/src/cpp/session/include/session/SessionConstants.hpp

+++ b/src/cpp/session/include/session/SessionConstants.hpp

@@ -142,13 +142,13 @@

 #define kSessionTmpDir             "rstudio-rsession"

 #ifdef QUARTO_ENABLED

-# define kDefaultPandocPath        "bin/quarto/bin/tools"

+# define kDefaultPandocPath        "@pandoc@"

 #else

 # define kDefaultPandocPath        "bin/pandoc"

 #endif

 #define kDefaultNodePath           "bin/node"

-#define kDefaultQuartoPath         "bin/quarto"

+#define kDefaultQuartoPath         "@quarto@"

 #define kDefaultRsclangPath        "bin/rsclang"

 #ifdef _WIN32